I don't get what the fuss is about. I'm right now using my Logitech F310 controller with the exact same configuration set with JoyToKey. It works great. I haven't had any accidental double-clicks or anything like that. Even if they did, do you have any idea how annoying it would be if this happened to PageUp/PageDown/Home/End? I don't have my pandora yet, but I believe the layout is A = Home, B = End, X = PgDn, Y = PgUp? If that's correct, imagine being a programmer and accidentally pressing PgUp when you only meant to press End. OK, not a big deal, but imagine having that happen to you every 5 minutes. Then you get an annoying scenario. OK, so you just put two of them on the nub, but then it's a bit counter-intuitive. Normally, those four keys are grouped together.
Another thing to note: you can click with the touch screen. You can't as easily press Home/End/PgUp/PgDn with the touch screen. This seems to me in and of itself to be a compelling enough reason to keep the current layout as the default.
The only reason I can think of to change the defaults is if the nub is really so terrible that this layout causes real issues, and if so, maybe the nubs need to be fixed, rather than being touted as the second-best nubs on the market? Just sayin'.